Distinct modes of SMAD2 chromatin binding and remodeling shape the transcriptional response to NODAL/Activin signaling

Pioneer factors and ATP-dependent chromatin remodeling factors interact dynamically: A new perspective

(2016) Erin E. Swinstead et al.   BIOESSAYS

Brachyury and SMAD signalling collaboratively orchestrate distinct mesoderm and endoderm gene regulatory networks in differentiating human embryonic stem cells

(2015) T. Faial et al.   DEVELOPMENT

Activin/Nodal signaling and NANOG orchestrate human embryonic stem cell fate decisions by controlling the H3K4me3 chromatin mark

(2015) Alessandro Bertero et al.   GENES & DEVELOPMENT

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

H3S28 phosphorylation is a hallmark of the transcriptional response to cellular stress

(2014) Anna Sawicka et al.   GENOME RESEARCH

TGF-β signaling to chromatin: How Smads regulate transcription during self-renewal and differentiation

(2014) Tessa Gaarenstroom et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Ten years of next-generation sequencing technology

(2014) Erwin L. van Dijk et al.   TRENDS IN GENETICS

Tyrosine phosphorylation of RNA polymerase II CTD is associated with antisense promoter transcription and active enhancers in mammalian cells

(2014) Nicolas Descostes et al.   eLife

Latent Enhancers Activated by Stimulation in Differentiated Cells

(2013) Renato Ostuni et al.   CELL

Morphogen interpretation: the transcriptional logic of neural tube patterning

(2013) Michael Cohen et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Modification of Enhancer Chromatin: What, How, and Why?

(2013) Eliezer Calo et al.   MOLECULAR CELL

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates

(2013) Li Shen et al.   PLoS One

Switch Enhancers Interpret TGF-β and Hippo Signaling to Control Cell Fate in Human Embryonic Stem Cells

(2013) Tobias A. Beyer et al.   Cell Reports

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells

(2012) Krishanpal Karmodiya et al.   BMC GENOMICS

The SMAD2/3 corepressor SNON maintains pluripotency through selective repression of mesendodermal genes in human ES cells

(2012) N. Tsuneyoshi et al.   GENES & DEVELOPMENT

The Chromatin Fingerprint of Gene Enhancer Elements

(2012) Gabriel E. Zentner et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Transforming Growth Factor   Inhibits Bone Morphogenetic Protein-Induced Transcription through Novel Phosphorylated Smad1/5-Smad3 Complexes

(2012) E. Gronroos et al.   MOLECULAR AND CELLULAR BIOLOGY

Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA

(2012) Jeremy M Simon et al.   Nature Protocols

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

Master Transcription Factors Determine Cell-Type-Specific Responses to TGF-β Signaling

(2011) Alan C. Mullen et al.   CELL

Paused RNA Polymerase II as a Developmental Checkpoint

(2011) Michael Levine   CELL

Spatiotemporal mechanisms of morphogen gradient interpretation

(2011) Marcos Nahmad et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Chromatin and transcriptional signatures for Nodal signaling during endoderm formation in hESCs

(2011) Si Wan Kim et al.   DEVELOPMENTAL BIOLOGY

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions

(2011) Gabriel E. Zentner et al.   GENOME RESEARCH

Activin/Nodal Signaling Controls Divergent Transcriptional Networks in Human Embryonic Stem Cells and in Endoderm Progenitors

(2011) Stephanie Brown et al.   STEM CELLS

Combinatorial assembly and function of chromatin regulatory complexes

(2011) Martin Lange et al.   Epigenomics

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

(2010) Lihua J Zhu et al.   BMC BIOINFORMATICS

TMEPAI, a Transmembrane TGF-β-Inducible Protein, Sequesters Smad Proteins from Active Participation in TGF-β Signaling

(2010) Yukihide Watanabe et al.   MOLECULAR CELL

Nodal Signaling Recruits the Histone Demethylase Jmjd3 to Counteract Polycomb-Mediated Repression at Target Genes

(2010) O. Dahle et al.   Science Signaling

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

TGF-β Superfamily Signaling in Embryonic Development and Homeostasis

(2009) Mary Y. Wu et al.   DEVELOPMENTAL CELL

Making a commitment: cell lineage allocation and axis patterning in the early mouse embryo

(2009) Sebastian J. Arnold et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Nodal Morphogens

(2009) A. F. Schier   Cold Spring Harbor Perspectives in Biology

Ski and SnoN, potent negative regulators of TGF-β signaling

(2008) Julien Deheuninck et al.   CELL RESEARCH

Genome-Wide Identification of Smad/Foxh1 Targets Reveals a Role for Foxh1 in Retinoic Acid Regulation and Forebrain Development

(2008) Cristoforo Silvestri et al.   DEVELOPMENTAL CELL

Essential Role of Chromatin Remodeling Protein Bptf in Early Mouse Embryos and Embryonic Stem Cells

(2008) Joseph Landry et al.   PLoS Genetics

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

How the Smads regulate transcription

(2007) Sarah Ross et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY